Analysis Summary
24
Total Visium Samples
(ONT: 11, SR: 13)
15
Genes Validated (scRNA)
194
Significant PSI Events
Validation Tier Summary
Validation Tiers:
TIER1_FULL Strong spatial + scRNA validation
TIER2_SPATIAL Reproducible spatial patterns only
TIER3_SCRNA scRNA validation but limited spatial
TIER4_PARTIAL Partial evidence in either modality
Key Findings
VCAN (Versican): Shows near-complete isoform switching (99% ΔPSI) between macrophages and tumor cells. The largest splicing effect in the dataset, validated both spatially (8/13 SR samples significant) and in scRNA-seq (p=1.4e-180).
APP (Amyloid Precursor Protein): Exon 7/8 inclusion varies dramatically between tumor states (MES: 82% vs NPC: 27%). Spatial HSIC-IR significant in 4/7 samples.
CLU (Clusterin): Most reproducible spatial isoform variation, significant in ALL 11 ONT samples (100%) and validated in scRNA-seq with 26 differential events.
scRNA-seq Differential Splicing
32,304 cells from glioma scRNA-seq dataset. PSI values quantified by MARVEL.
| Gene |
Event Type |
State 1 |
State 2 |
PSI 1 |
PSI 2 |
ΔPSI |
padj |
Main Figures
Fig1 App Psi By Tumor State
Fig1 App Psi Boxplot
Fig2 Vcan Psi By Tumor State
Fig2 Vcan Psi Boxplot
Fig3 Clu Visium Hsic Ir
Fig4 Spatial Isoform Switching
Fig5 Spatial Isoform Zh1019T1
SpaCET Deconvolution Plots
Cell type deconvolution showing VCAN isoform correlations with tumor vs macrophage content.
Spacet Mgh258 Macro
Spacet Zh1007Inf Macro
Spacet Zh1007Nec Macro
Spacet Zh1019T1 Macro
Spacet Zh1019Inf Macro
Spacet Zh8811Abulk Macro
Spacet Zh8811Bbulk Macro
Spacet Zh8812Bulk Macro
Spacet Zh881T1 Macro
Spacet Zh881Inf Macro
Spacet Zh916T1 Macro
Spacet Zh916Bulk Macro
Spacet Zh916Inf Macro
Spatial Isoform Maps
Spatial distribution of isoform ratios across tissue sections.
Spatial Isoform Mgh258
Spatial Isoform Zh1007Inf
Spatial Isoform Zh1007Nec
Spatial Isoform Zh1019T1
Spatial Isoform Zh1019Inf
Spatial Isoform Zh8811Abulk